Hi Thanks for the help.
To clarify my ideas, when I do
> desc pdbname.REA
RESIDUE name: REA
RESIDUE sequence number: 1
RESIDUE PDB sequence number: 1
Type: undefined
Connection atoms:
Connect atom 0: A<N73 1>
Connect atom 1: A<N75 76>
Improper torsions:
Contents:
A<N75 76>
A<H69 75>
A<H68 74>
A<C67 73>
A<H57 72>
etc
do I have to do in tleap: bond pdbname.REA.N75 pdbname.REB.C2
I amnot sure if I should put N75 here or N76, N75 being the atom name (A<N75
76>) while 76 is its number!
thanks again
________________________________
From: ros <ros.servidor.unam.mx>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Thu, July 22, 2010 7:06:19 PM
Subject: Re: [AMBER] question about bond command
Yes, you can use the bond command to bond specific atoms of each residue:
In tleap:
>Bond pdb1.res1.atom# pdb2.res2.atom#
You can check the listing of resname and atom # with:
>desc pdbname
Hope it helps!
Have a good day
Rodrigo
--------------
Depto de Fisicoquimica
Instituto de Quimica
UNAM
2010/7/22, Philippe Pinard <pp_amber17.yahoo.com>:
> Hi Amber users
>
> I have a quite large organic molecule (2000 atoms) that I represented in
> terms
> of 4 different residues (rea, reb, rec, red). These residues lib and frcmod
> were
> built using antechamber.
> Of course the molecule is composed of these residues (30 rea, 40 reb, 50
> rec,
> and 30 red) that are bonded in a certain way.
> I want to know whether I should use bond command to bond the residues to
> each
> other?
>
> Regards
>
> Philippe
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Enviado desde mi dispositivo móvil
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Received on Thu Jul 22 2010 - 12:00:03 PDT
